For now, there are two workarounds, but no real possibility to set the subpixel rendering to BGR.
chrome://flags and set the flags stated below to the specified values.
Disable DirectWrite completely and use the old GDI drawing methods.
You can completely disable the new rendering method and use the old one as in pre-36.
Disable DirectWrite: set it to Enable
Use grayscale subpixel rendering instead of red and blue
Keep using DirectWrite, but subpixeling will not use red and blue, but grayscale colors instead.
LCD text antialiasing: set it to Disabled
Restart Chrome and you will see the changes.
EDIT: A recent comment around my bug reports says it will be fixed in the upcoming Chrome versions.